X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceFeatureTest.java;h=673ea290a7e74ca7c1de3e7d04fc56e528060624;hb=5a631296dd1dcc1df7b50487a647c27333696c74;hp=d105cc5d2721d9196693c84d4ce3cb0faa199eaf;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index d105cc5..673ea29 100644
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -26,11 +26,11 @@ import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.gui.JvOptionPane;
-
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+
public class SequenceFeatureTest
{
@@ -42,13 +42,13 @@ public class SequenceFeatureTest
}
@Test(groups = { "Functional" })
- public void testCopyConstructor()
+ public void testCopyConstructors()
{
SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
12.5f, "group");
sf1.setValue("STRAND", "+");
sf1.setValue("Note", "Testing");
- Integer count = new Integer(7);
+ Integer count = Integer.valueOf(7);
sf1.setValue("Count", count);
SequenceFeature sf2 = new SequenceFeature(sf1);
@@ -56,10 +56,41 @@ public class SequenceFeatureTest
assertEquals("desc", sf2.getDescription());
assertEquals(22, sf2.getBegin());
assertEquals(33, sf2.getEnd());
+ assertEquals(12.5f, sf2.getScore());
assertEquals("+", sf2.getValue("STRAND"));
assertEquals("Testing", sf2.getValue("Note"));
// shallow clone of otherDetails map - contains the same object values!
assertSame(count, sf2.getValue("Count"));
+
+ /*
+ * copy constructor modifying begin/end/group/score
+ */
+ SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f);
+ assertEquals("type", sf3.getType());
+ assertEquals("desc", sf3.getDescription());
+ assertEquals(11, sf3.getBegin());
+ assertEquals(14, sf3.getEnd());
+ assertEquals(17.4f, sf3.getScore());
+ assertEquals("+", sf3.getValue("STRAND"));
+ assertEquals("Testing", sf3.getValue("Note"));
+ // shallow clone of otherDetails map - contains the same object values!
+ assertSame(count, sf3.getValue("Count"));
+
+ /*
+ * copy constructor modifying type/begin/end/group/score
+ */
+ SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12,
+ 15, "group3", -9.1f);
+ assertEquals("Disulfide bond", sf4.getType());
+ assertTrue(sf4.isContactFeature());
+ assertEquals("desc", sf4.getDescription());
+ assertEquals(12, sf4.getBegin());
+ assertEquals(15, sf4.getEnd());
+ assertEquals(-9.1f, sf4.getScore());
+ assertEquals("+", sf4.getValue("STRAND"));
+ assertEquals("Testing", sf4.getValue("Note"));
+ // shallow clone of otherDetails map - contains the same object values!
+ assertSame(count, sf4.getValue("Count"));
}
/**
@@ -75,7 +106,7 @@ public class SequenceFeatureTest
assertEquals("+", sf1.getValue("STRAND"));
assertNull(sf1.getValue("strand")); // case-sensitive
assertEquals(".", sf1.getValue("unknown", "."));
- Integer i = new Integer(27);
+ Integer i = Integer.valueOf(27);
assertSame(i, sf1.getValue("Unknown", i));
}
@@ -242,4 +273,50 @@ public class SequenceFeatureTest
"group");
assertTrue(sf.isContactFeature());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetDetailsReport()
+ {
+ SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
+ String seqName = seq.getName();
+
+ // single locus, no group, no score
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
+ String expected = "
Location | TestSeq | 22 |
"
+ + "Type | variant | |
"
+ + "Description | G,C | |
";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ // contact feature
+ sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+ null);
+ expected = "
Location | TestSeq | 28:31 |
"
+ + "Type | Disulphide Bond | |
"
+ + "Description | a description | |
";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ sf = new SequenceFeature("variant", "G,C", 22, 33,
+ 12.5f, "group");
+ sf.setValue("Parent", "ENSG001");
+ sf.setValue("Child", "ENSP002");
+ expected = "
Location | TestSeq | 22-33 |
"
+ + "Type | variant | |
"
+ + "Description | G,C | |
"
+ + "Score | 12.5 | |
"
+ + "Group | group | |
"
+ + "Child | | ENSP002 |
"
+ + "Parent | | ENSG001 |
";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ /*
+ * feature with embedded html link in description
+ */
+ String desc = "Fer2 Status: True Positive Pfam 8_8";
+ sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
+ expected = "
Location | TestSeq | 8-83 |
"
+ + "Type | Pfam | |
"
+ + "Description | Fer2 Status: True Positive Pfam 8_8 | |
"
+ + "Group | Uniprot | |
";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+ }
}